change name

tasks/multiqc.wdl

 task multiqc {
 
-	Array[File]? read1_zip
-	Array[File]? read2_zip
+	Array[File] read1_zip
+	Array[File] read2_zip
 
-	Array[File]? txt1
-	Array[File]? txt2
+	Array[File] txt1
+	Array[File] txt2
 
 	Array[File] summary
 
-	Array[File]? zip
-
 	String docker
 	String cluster_config
 	String disk_size
 	command <<<
 		set -o pipefail
 		set -e
-		if [ ${zip} ];then
-			mkdir -p /cromwell_root/tmp/fastqc
-			mkdir -p /cromwell_root/tmp/fastqscreen
-			mkdir -p /cromwell_root/tmp/benchmark
-
-			cp ${sep=" " read1_zip} ${sep=" " read2_zip} /cromwell_root/tmp/fastqc
-			cp ${sep=" " txt1} ${sep=" " txt2} /cromwell_root/tmp/fastqscreen
-			cp ${sep=" " summary} /cromwell_root/tmp/benchmark
-
-			multiqc /cromwell_root/tmp/
-
-			cat multiqc_data/multiqc_general_stats.txt > multiqc_general_stats.txt
-			cat multiqc_data/multiqc_fastq_screen.txt > multiqc_fastq_screen.txt
-			cat multiqc_data/multiqc_happy_data.json > multiqc_happy_data.json
-		else
-			mkdir -p /cromwell_root/tmp/benchmark
-			cp ${sep=" " summary} /cromwell_root/tmp/benchmark
-			multiqc /cromwell_root/tmp/
-			cat multiqc_data/multiqc_happy_data.json > multiqc_happy_data.json
-		fi
+		mkdir -p /cromwell_root/tmp/fastqc
+		mkdir -p /cromwell_root/tmp/fastqscreen
+		mkdir -p /cromwell_root/tmp/benchmark
+
+		cp ${sep=" " read1_zip} ${sep=" " read2_zip} /cromwell_root/tmp/fastqc
+		cp ${sep=" " txt1} ${sep=" " txt2} /cromwell_root/tmp/fastqscreen
+		cp ${sep=" " summary} /cromwell_root/tmp/benchmark
+
+		multiqc /cromwell_root/tmp/
+
+		cat multiqc_data/multiqc_general_stats.txt > multiqc_general_stats.txt
+		cat multiqc_data/multiqc_fastq_screen.txt > multiqc_fastq_screen.txt
+		cat multiqc_data/multiqc_happy_data.json > multiqc_happy_data.json
 	
 	>>>
 

workflow.wdl

 			input: 
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			group="D5",
-			sample="D5",
+			group="LCL5",
+			sample="LCL5",
 			pl="ILLUMINAL",
 			fasta=fasta,
 			ref_dir=ref_dir,
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			sorted_bam=mapping_D5.sorted_bam,
 			sorted_bam_index=mapping_D5.sorted_bam_index,
-			sample="D5",
+			sample="LCL5",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			Dedup_bam=Dedup_D5.Dedup_bam,
 			Dedup_bam_index=Dedup_D5.Dedup_bam_index,
-			sample="D5",
+			sample="LCL5",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			wgs_metrics_algo=deduped_Metrics_D5.deduped_wgsmetrics,
 			aln_metrics=deduped_Metrics_D5.dedeuped_aln_metrics,
 			is_metrics=deduped_Metrics_D5.deduped_is_metrics,
-			sample="D5",
+			sample="LCL5",
 			docker=SENTIEONdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size		
 			Dedup_bam_index=Dedup_D5.Dedup_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
-			sample="D5",
+			sample="LCL5",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample="D5",
+			sample="LCL5",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			recaled_bam=BQSR_D5.recaled_bam,
 			recaled_bam_index=BQSR_D5.recaled_bam_index,
-			sample="D5",
+			sample="LCL5",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			input: 
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			group="D6",
-			sample="D6",
+			group="LCL6",
+			sample="LCL6",
 			pl="ILLUMINAL",
 			fasta=fasta,
 			ref_dir=ref_dir,
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			sorted_bam=mapping_D6.sorted_bam,
 			sorted_bam_index=mapping_D6.sorted_bam_index,
-			sample="D6",
+			sample="LCL6",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			Dedup_bam=Dedup_D6.Dedup_bam,
 			Dedup_bam_index=Dedup_D6.Dedup_bam_index,
-			sample="D6",
+			sample="LCL6",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			wgs_metrics_algo=deduped_Metrics_D6.deduped_wgsmetrics,
 			aln_metrics=deduped_Metrics_D6.dedeuped_aln_metrics,
 			is_metrics=deduped_Metrics_D6.deduped_is_metrics,
-			sample="D6",
+			sample="LCL6",
 			docker=SENTIEONdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size		
 			Dedup_bam_index=Dedup_D6.Dedup_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
-			sample="D6",
+			sample="LCL6",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample="D6",
+			sample="LCL6",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			recaled_bam=BQSR_D6.recaled_bam,
 			recaled_bam_index=BQSR_D6.recaled_bam_index,
-			sample="D6",
+			sample="LCL6",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			input: 
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			group="F7",
-			sample="F7",
+			group="LCL7",
+			sample="LCL7",
 			pl="ILLUMINAL",
 			fasta=fasta,
 			ref_dir=ref_dir,
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			sorted_bam=mapping_F7.sorted_bam,
 			sorted_bam_index=mapping_F7.sorted_bam_index,
-			sample="F7",
+			sample="LCL7",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			Dedup_bam=Dedup_F7.Dedup_bam,
 			Dedup_bam_index=Dedup_F7.Dedup_bam_index,
-			sample="F7",
+			sample="LCL7",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			wgs_metrics_algo=deduped_Metrics_F7.deduped_wgsmetrics,
 			aln_metrics=deduped_Metrics_F7.dedeuped_aln_metrics,
 			is_metrics=deduped_Metrics_F7.deduped_is_metrics,
-			sample="F7",
+			sample="LCL7",
 			docker=SENTIEONdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size		
 			Dedup_bam_index=Dedup_F7.Dedup_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
-			sample="F7",
+			sample="LCL7",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample="F7",
+			sample="LCL7",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			recaled_bam=BQSR_F7.recaled_bam,
 			recaled_bam_index=BQSR_F7.recaled_bam_index,
-			sample="F7",
+			sample="LCL7",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			input: 
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			group="M8",
-			sample="M8",
+			group="LCL8",
+			sample="LCL8",
 			pl="ILLUMINAL",
 			fasta=fasta,
 			ref_dir=ref_dir,
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			sorted_bam=mapping_M8.sorted_bam,
 			sorted_bam_index=mapping_M8.sorted_bam_index,
-			sample="M8",
+			sample="LCL8",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			Dedup_bam=Dedup_M8.Dedup_bam,
 			Dedup_bam_index=Dedup_M8.Dedup_bam_index,
-			sample="M8",
+			sample="LCL8",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			wgs_metrics_algo=deduped_Metrics_M8.deduped_wgsmetrics,
 			aln_metrics=deduped_Metrics_M8.dedeuped_aln_metrics,
 			is_metrics=deduped_Metrics_M8.deduped_is_metrics,
-			sample="M8",
+			sample="LCL8",
 			docker=SENTIEONdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size		
 			Dedup_bam_index=Dedup_M8.Dedup_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
-			sample="M8",
+			sample="LCL8",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample="M8",
+			sample="LCL8",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			recaled_bam=BQSR_M8.recaled_bam,
 			recaled_bam_index=BQSR_M8.recaled_bam_index,
-			sample="M8",
+			sample="LCL8",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 
 	    Array[File] benchmark_summary = [benchmark_D5.summary, benchmark_D6.summary, benchmark_F7.summary, benchmark_M8.summary]
 
-	    Array[File] qualimap_zip = [qualimap_D5.zip, qualimap_D6.zip, qualimap_F7.zip, qualimap_M8.zip]
-
-
 		call multiqc.multiqc as multiqc_big {
 			input:
 			read1_zip=fastqc_read1_zip,
 			txt1=fastqscreen_txt1,
 			txt2=fastqscreen_txt2,
 			summary=benchmark_summary,
-			zip=qualimap_zip,
 			docker=MULTIQCdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size